sys.exit()
elif opt in ('-r',"--filerank"):
fr = int(arg)-1
elif opt in ('-i','--inputdir'):
inputdir = arg
if inputdir[-1] != '/':
inputdir += '/'
elif opt in ('-o','--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
hashobject = Fastq_Reader(inputdir,outputdir)
Hashq_Files = glob.glob(os.path.join(hashobject.input_path,'*.hashq.*'))
hashobject.infile = Hashq_Files[fr]
hashobject.outfile = hashobject.output_path + 'intermediate_clusters/' + str(fr)
hashobject.global_weights = np.load(hashobject.output_path + 'global_weights.npy')
global_weight_sum = hashobject.global_weights.sum(dtype=np.float64)
Cluster_Files = glob.glob(os.path.join(hashobject.output_path,'*.cluster.npy'))
Cluster_Files = [(int(cf[cf.rfind('/')+1:cf.index('.')]),cf) for cf in Cluster_Files]
cluster_sizes = np.load(hashobject.output_path+'kmer_cluster_sizes.npy')
total_set_size = 0
cluster_weights = []
cluster_keys = []
outpart = 0
for ci,cf in Cluster_Files:
# ignore super clusters and super small clusters
if cluster_sizes[ci] < 0.2*2**hashobject.hash_size:
cw = np.load(cf)
cw_sum_prob = hashobject.global_weights[cw].sum(dtype=np.float64)/global_weight_sum
if cw_sum_prob > 0.00002:
cluster_weights.append((set(cw),cw_sum_prob))
